COVID-19 patients, deaths, and death rate
05/02/2020
1 Source of the data
The data is compiled from https://github.com/CSSEGISandData/COVID-19.
The python script script.py is a modification of https://github.com/JacopoPan/JHU-2019nCoV-to-pandas-DF
Here I avoided any data modeling and am just showing the raw number of diagnosed patients, deaths, death rate, new cases by day, and new deaths by day.
2 Top countries by cases and deaths
deathmat = read.csv("deaths.tsv", header=T,
sep="\t", check.names=F, row.names=1)
countdeath = apply(deathmat[nrow(deathmat),1:(ncol(deathmat) - 1)], 2, sum)
casemat = read.csv("confirmed.tsv",
header=T, sep="\t", check.names=F, row.names=1)
countcases = apply(casemat[nrow(casemat),1:(ncol(casemat) - 1)], 2, sum)
totaldf = data.frame(Countries=c(names(countdeath), names(countcases)),
Values=as.numeric(c(countdeath, countcases)),
Variable=c(rep("Deaths", length(countdeath)),
rep("Diagnosed", length(countcases))))
select_countries = names(sort(countcases, TRUE))[1:20]
totaldf = totaldf[totaldf$Countries %in% select_countries, ]
totaldf$Countries = factor(totaldf$Countries, levels=select_countries)
P = ggplot(totaldf, aes(x=Countries, y=Values, fill=Variable)) +
geom_bar(stat="identity", position="dodge") +
facet_wrap(~Variable, nrow=2, scales="free") +
theme_bw(base_size=18) +
scale_y_log10("Number of patients", labels=comma) +
theme(legend.position="bottom",
axis.text.x=element_text(angle=45, hjust=1)) +
annotation_logticks(sides="lr")
plot(P)
2.1 Calculate doubling rate for each country since April 15th
Red line will show daily increase of twice.
Purple line will show daily increase of 10%
Blue line will show daily increase of 1%
get_expected = function(datadf, rate=2, init=100){
list.data = lapply(unique(datadf$variable), function(country){
tempdf = datadf[datadf$variable==country, ]
# idx_st = min(which(tempdf$value >= init))
idx_st = min(which(tempdf$date >= as.Date("2020-04-15")))
init_val = tempdf$value[idx_st]
advals = sapply(1:nrow(tempdf), function(x){
if(x > idx_st){
return(init_val * (rate**(x - idx_st)))
}else{
return(0)
}
})
ad_df = data.frame(variable=country, Rate=rate,
date=tempdf$date, value=advals)
return(ad_df)
})
out_df = do.call("rbind", list.data)
return(out_df)
}3 Total morbidity
deathmat = read.csv("deaths.tsv", header=T,
sep="\t", check.names=F, row.names=1)
countries = c("China", "Iran", "Italy",
"US", "Russia", "Spain",
"France", "Canada", "Germany",
"Korea, South", "United Kingdom", "Israel")
deathmat = deathmat[,c(countries, "date")]
moltendf = melt(deathmat)## Using date as id variablesmoltendf$date = as.Date(moltendf$date)
doubling_df = get_expected(moltendf, rate=2, init=100)
onepercent_df = get_expected(moltendf, rate=1.01, init=100)
tenpercent_df = get_expected(moltendf, rate=1.1, init=100)
P2 = ggplot(moltendf[moltendf$value > 0,],
aes(x=date, y=(value),
group=variable)) +
geom_line() +
geom_line(data=doubling_df[doubling_df$value > 0,], colour="red3", linetype=2) +
geom_line(data=onepercent_df[onepercent_df$value > 0,], colour="blue", linetype=3) +
geom_line(data=tenpercent_df[tenpercent_df$value > 0,], colour="purple", linetype=4) +
theme_bw(base_size=14) +
facet_wrap(~variable) +
scale_y_log10(
name="Total deaths caused by SARS-CoV-2", labels=comma, limits=c(1, max(moltendf$value))) +
xlab("Date as of outbreak") +
ggtitle(paste("Last update on", Sys.time())) +
annotation_logticks()
plot(P2)## Warning: Removed 146 row(s) containing missing values (geom_path).## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?
## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?## Warning: Removed 21 row(s) containing missing values (geom_path).
4 New deaths by day
list.data = lapply(colnames(deathmat)[1:(ncol(deathmat)-1)], function(country){
new_cases = diff(deathmat[,country])
addf = data.frame(date=deathmat$date[2:nrow(deathmat)],
variable=country,
value=new_cases)
})
moltendf = do.call("rbind", list.data)
moltendf$date = as.Date(moltendf$date)
P = ggplot(moltendf, aes(x=date, y=value, group=variable)) +
geom_line() +
theme_bw(base_size=14) +
facet_wrap(~variable, scales="free") +
scale_y_continuous(
name="New deaths caused by SARS-CoV-2", labels=comma) +
ggtitle(paste("Last update on", Sys.time())) +
xlab("Date as of outbreak")
plot(P)
5 Total COVID-19 patients
casemat = read.csv("confirmed.tsv",
header=T, sep="\t", check.names=F, row.names=1)
casemat = casemat[,c(countries, "date")]
moltendf = melt(casemat)## Using date as id variablesmoltendf$date = as.Date(moltendf$date)
doubling_df = get_expected(moltendf, rate=2, init=100)
onepercent_df = get_expected(moltendf, rate=1.01, init=100)
tenpercent_df = get_expected(moltendf, rate=1.1, init=100)
P2 = ggplot(moltendf[moltendf$value > 0, ], aes(x=date, y=(value), group=variable)) +
geom_line() +
theme_bw(base_size=14) +
facet_wrap(~variable) +
geom_line(data=doubling_df[doubling_df$value > 0,], colour="red3", linetype=2) +
geom_line(data=onepercent_df[onepercent_df$value > 0,], colour="blue", linetype=3) +
geom_line(data=tenpercent_df[tenpercent_df$value > 0,], colour="purple", linetype=4) +
scale_y_log10(
name="Total COVID-19 patients", labels=comma, limits=c(1, max(moltendf$value))) +
xlab("Date as of outbreak") +
ggtitle(paste("Last update on", Sys.time())) +
annotation_logticks()
plot(P2)## Warning: Removed 151 row(s) containing missing values (geom_path).## Warning: Removed 11 row(s) containing missing values (geom_path).
5.1 New COVID-19 patients by day
list.data = lapply(colnames(casemat)[1:(ncol(casemat)-1)], function(country){
new_cases = diff(casemat[,country])
addf = data.frame(date=casemat$date[2:nrow(casemat)],
variable=country,
value=new_cases)
})
moltendf = do.call("rbind", list.data)
moltendf$date = as.Date(moltendf$date)
P = ggplot(moltendf, aes(x=date, y=value, group=variable)) +
geom_line() +
theme_bw(base_size=14) +
facet_wrap(~variable, scales="free") +
scale_y_continuous(
name="New COVID-19 patients", labels=comma) +
ggtitle(paste("Last update on", Sys.time())) +
xlab("Date as of outbreak")
plot(P)
5.2 PCA of countries by total patients
Principal component analysis identifies non-correlating variables (components) from the data and here can identify outlier countries according to a single variable.
In the following plots, I show the first three principal components for total diagnosed patients by day, total deaths by day, and also death rate by day.
casemat = read.csv("confirmed.tsv", header=T, sep="\t", check.names=F, row.names=1)
pcamat = casemat[,1:(ncol(casemat) - 1)]
PCA = prcomp(t(pcamat))
pcadf = as.data.frame(PCA$x)
pcadf$Country = colnames(casemat)[1:nrow(pcadf)]
pcadf$Show = ifelse(pcadf$Country %in% countries, TRUE, FALSE)
P = ggplot(pcadf, aes(x=PC1, y=PC2)) +
geom_point(aes(colour=Show, shape=Show), alpha=0.5) +
geom_text_repel(data=pcadf[pcadf$Show,], aes(label=Country), colour="blue", size=4) +
theme_bw(base_size=14) +
xlab("First principal component") +
ylab("Second principal component") +
ggtitle(paste("Last update on", Sys.time())) +
theme(legend.position="bottom")
plot(P)
P = ggplot(pcadf, aes(x=PC2, y=PC3)) +
geom_point(aes(colour=Show, shape=Show), alpha=0.5) +
geom_text_repel(data=pcadf[pcadf$Show,], aes(label=Country), colour="blue", size=4) +
theme_bw(base_size=14) +
ylab("Third principal component") +
xlab("Second principal component") +
ggtitle(paste("Last update on", Sys.time())) +
theme(legend.position="bottom")
plot(P)
5.3 PCA of countries by morbidity
deathmat = read.csv("deaths.tsv", header=T,
sep="\t", check.names=F, row.names=1)
pcamat = deathmat[,1:(ncol(deathmat) - 1)]
PCA = prcomp(t(pcamat))
pcadf = as.data.frame(PCA$x)
pcadf$Country = colnames(deathmat)[1:nrow(pcadf)]
pcadf$Show = ifelse(pcadf$Country %in% countries, TRUE, FALSE)
P = ggplot(pcadf, aes(x=PC1, y=PC2)) +
geom_point(aes(colour=Show, shape=Show), alpha=0.5) +
geom_text_repel(data=pcadf[pcadf$Show,], aes(label=Country), colour="blue", size=4) +
theme_bw(base_size=14) +
xlab("First principal component") +
ylab("Second principal component") +
ggtitle(paste("Last update on", Sys.time())) +
theme(legend.position="bottom")
plot(P)
P = ggplot(pcadf, aes(x=PC2, y=PC3)) +
geom_point(aes(colour=Show, shape=Show), alpha=0.5) +
geom_text_repel(data=pcadf[pcadf$Show,], aes(label=Country), colour="blue", size=4) +
theme_bw(base_size=14) +
ylab("Third principal component") +
xlab("Second principal component") +
ggtitle(paste("Last update on", Sys.time())) +
theme(legend.position="bottom")
plot(P)
5.4 Death rate
The two countries which succeeded in stopping the spread, China and South Korea, provide the most accurate measurement of true death rate. In the death rate plot below, the range of the death rate of these two countries is shown by pink.
deathmat = read.csv("deaths.tsv", header=T,
sep="\t", check.names=F, row.names=1)
casemat = read.csv("confirmed.tsv", header=T, sep="\t", check.names=F, row.names=1)
deathrate = deathmat[,1:(ncol(deathmat) - 1)] / (0.1 + casemat[,setdiff(colnames(deathmat), "date")])
deathratedf = deathrate
deathratedf$date = casemat$date
moltendf = melt(deathratedf[,c(countries, "date")])## Using date as id variablesmoltendf$date = as.Date(moltendf$date)
moltendf$Label = NA
deathratedf$date = as.Date(deathratedf$date)
textmat = casemat[which.max(casemat[,"China"]), ]
textdf = melt(as.data.frame(textmat[,c(countries, "date")]))## Using date as id variablestextdf$date = min(as.Date(deathratedf$date)) + 10
textdf$Label = paste("N =", comma(textdf$value))
textdf$value = 0.08
P = ggplot(moltendf, aes(x=date, y=value, group=variable)) +
geom_rect(xmin=min(deathratedf$date),
xmax=max(deathratedf$date+1),
ymin=max(deathratedf$China),
ymax=max(deathratedf[,"Korea, South"]),
alpha=0.05,
fill="pink") +
geom_line() +
geom_text(data=textdf, aes(x=date, y=value, label=Label), colour='blue') +
theme_bw(base_size=14) +
facet_wrap(~variable, scales="free") +
scale_y_continuous(
name=expression("COVID-19 daily "*frac("deaths", "cases")),
labels=comma) +
xlab("Date as of outbreak") +
ggtitle(paste("Last update on", Sys.time())) +
coord_cartesian(ylim=c(0, 0.2))
plot(P)
pcamat = deathrate
PCA = prcomp(t(pcamat))
pcadf = as.data.frame(PCA$x)
pcadf$Country = colnames(deathmat)[1:nrow(pcadf)]
pcadf$Show = ifelse(pcadf$Country %in% countries, TRUE, FALSE)
P = ggplot(pcadf, aes(x=PC1, y=PC2)) +
geom_point(aes(colour=Show, shape=Show), alpha=0.5) +
geom_text_repel(data=pcadf[pcadf$Show,], aes(label=Country), colour="blue", size=4) +
theme_bw(base_size=14) +
xlab("First principal component") +
ylab("Second principal component") +
theme(legend.position="bottom")
plot(P)
P = ggplot(pcadf, aes(x=PC2, y=PC3)) +
geom_point(aes(colour=Show, shape=Show), alpha=0.5) +
geom_text_repel(data=pcadf[pcadf$Show,], aes(label=Country), colour="blue", size=4) +
theme_bw(base_size=14) +
ylab("Third principal component") +
xlab("Second principal component") +
theme(legend.position="bottom")
plot(P)
6 Canada
casepath = "COVID-19/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv"
casedf = read.csv(casepath, header=T, check.names=F)
casedf = casedf[casedf[,2]=="Canada", c(1, 5:ncol(casedf))]
provinces = casedf[apply(casedf[,2:ncol(casedf)], 1, sum) > 0, 1]
casedf = casedf[casedf[,1] %in% provinces,]
moltendf = melt(casedf)## Using Province/State as id variablesmoltendf$date = as.Date(as.character(moltendf$variable), tryFormats="%m/%d/%y")
moltendf$variable = moltendf[,"Province/State"]
doubling_df = get_expected(moltendf, rate=2, init=100)
doubling_df[,"Province/State"] = doubling_df$variable
onepercent_df = get_expected(moltendf, rate=1.01, init=100)
onepercent_df[,"Province/State"] = onepercent_df$variable
tenpercent_df = get_expected(moltendf, rate=1.1, init=100)
tenpercent_df[,"Province/State"] = tenpercent_df$variable
textdf = melt(casedf[,c(1, ncol(casedf))])## Using Province/State as id variablestextdf$date = as.Date(as.character(textdf$variable), tryFormats="%m/%d/%y")
textdf$date = min(as.Date(textdf$date)) - 50
textdf$Label = paste("N =", comma(round(textdf$value)))
textdf$value = 2000
P = ggplot(moltendf[moltendf$value > 0,], aes(x=date, y=value, group=`Province/State`)) +
geom_line() +
geom_line(data=doubling_df[doubling_df$value > 0,], colour="red3", linetype=2) +
geom_line(data=onepercent_df[onepercent_df$value > 0,], colour="blue", linetype=3) +
geom_line(data=tenpercent_df[tenpercent_df$value > 0,], colour="purple", linetype=4) +
geom_text(data=textdf, aes(label=Label), colour="blue") +
theme_bw(base_size=18) +
facet_wrap(~`Province/State`) +
scale_y_log10("Number of patients diagnosed with COVID-19", labels=comma, limits=c(1, max(moltendf$value))) +
xlab("Date as of global incidence")
plot(P)## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?## Warning: Removed 126 row(s) containing missing values (geom_path).## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?## Warning: Removed 14 row(s) containing missing values (geom_path).
6.1 Canada’s deaths
casepath = "COVID-19/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv"
casedf = read.csv(casepath, header=T, check.names=F)
casedf = casedf[casedf[,2]=="Canada", c(1, 5:ncol(casedf))]
provinces = casedf[apply(casedf[,2:ncol(casedf)], 1, sum) > 0, 1]
casedf = casedf[casedf[,1] %in% provinces,]
moltendf = melt(casedf)## Using Province/State as id variablesmoltendf$date = as.Date(as.character(moltendf$variable), tryFormats="%m/%d/%y")
moltendf$variable = moltendf[,"Province/State"]
doubling_df = get_expected(moltendf, rate=2, init=100)
doubling_df[,"Province/State"] = doubling_df$variable
onepercent_df = get_expected(moltendf, rate=1.01, init=100)
onepercent_df[,"Province/State"] = onepercent_df$variable
tenpercent_df = get_expected(moltendf, rate=1.1, init=100)
tenpercent_df[,"Province/State"] = tenpercent_df$variable
textdf = melt(casedf[,c(1, ncol(casedf))])## Using Province/State as id variablestextdf$date = as.Date(as.character(textdf$variable), tryFormats="%m/%d/%y")
textdf$date = min(as.Date(textdf$date)) - 5
textdf$Label = paste("N =", comma(round(textdf$value)))
textdf$value = max(moltendf$value)
P = ggplot(moltendf[moltendf$value > 0,], aes(x=date, y=value, group=`Province/State`)) +
geom_line() +
geom_line(data=doubling_df[doubling_df$value > 0,], colour="red3", linetype=2) +
geom_line(data=onepercent_df[onepercent_df$value > 0,], colour="blue", linetype=3) +
geom_line(data=tenpercent_df[tenpercent_df$value > 0,], colour="purple", linetype=4) +
geom_text(data=textdf, aes(label=Label), colour="blue") +
theme_bw(base_size=18) +
facet_wrap(~`Province/State`) +
scale_y_log10("Number of deaths due to COVID-19", labels=comma, limits=c(1, max(moltendf$value))) +
xlab("Date as of first Canadian death")
plot(P)## geom_path: Each group consists of only one observation. Do you need to adjust
## the group aesthetic?## Warning: Removed 87 row(s) containing missing values (geom_path).## Warning: Removed 2 row(s) containing missing values (geom_path).